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FreeSurfer: Open-source software for processing and analyzing brain MRI images (mgh.harvard.edu)
60 points by XzetaU8 10 days ago | hide | past | favorite | 19 comments

FreeSurfer is actually NOT open source.



Edit: and downvotes don't change reality. It's great software, but it's not open source.

Here's the source: https://github.com/freesurfer/freesurfer. It's open (according to most people's understanding of open), but it's not free for commercial use likely because of IP reasons and to avoid conflicts of interest when receiving funding from the NIH to continue development.

not free for commercial? the license is https://github.com/freesurfer/freesurfer/blob/dev/LICENSE.tx... . My reading of it says you can use it for commercial use and make derivative commercial products under your own license terms. The only thing it says is it is not FDA approved and should really only be used for research purposes, but you can do what you want, we don't accept any responsibility for your use of the software.

Large portions of FreeSurfer are covered by a different license which includes non-free terms such as

> (d) such use, reproduction, making of derivative works, display and distribution of the software is limited to non-commercial internal research and educational purposes by not-for-profit entities;

> (e) you may not use Freesurfer in research that is sponsored by a commercial entity;

> (g) you agree that this License Agreement may be terminated at any time by notice posted on Licensor applicable website if any contributor to Freesurfer with the legal right to do so demands that or compels Licensor to terminate this license.

i suspect the academic lab's definition of open source is more "loosey goosey", i.e., "is the technique published in a paper/poster and can it be reimplemented by our grad students/postdocs?" If so...Open Source(tm)!

The Open Source Definition doesn't include "free for non-commercial use" licenses.

In a few hours with FreeSurfer, you can go from a raw MRI image to a structured labeled set of data identifying the geometry of a subjects brain structures.

One of the interesting hacks is to inflate the cortical surface to a sphere which enables nonlinear registration to the accuracy of human experts.

I’m extremely impressed with the longevity of FreeSurfer, I just desperately wish it was extensible with different atlases.

It is extensible if you have the training set. A more recent criticism is that it only uses the curvature of the cortical surface to do its work, whereas more recent atlases such at the Glasser HCP use multimodal data.

Exactly this, I just want to use it with Glasser or the like but it's not really feasible. And since DKT just doesn't capture what we need, FreeSurfer gets left behind.

What does “extensible with different atlases” mean?

The idea predates modern usage, back to 1967: https://en.wikipedia.org/wiki/Talairach_coordinates, where they were trying to define a common way of referring to structures.

In this freesurfer sense it is the result of a training set, where an expert has delineated cortical and/or subcortical structure on a set of one or more images. If you have multiple images and you map them all into the same atlas space, you can derive a probabilistic model from this, or collapse it to a highest likelihood map or whatever you want.

The cortical and subcortical labeling algorithms used in freesurfer use such a (probabilistic) atlas as one of the inputs. GP is wishing that they could replace this with a new, presumably improved, version.

it's like what? 10-15 years now?

I have not really opened Freesurfer in ages...but unless they've really put effort into modernizing it, it's "UI" is best described as...."grad student" at best.

Still, it's better than AFNI...

I got to know Iman personally a little, and he's easily one of the smartest people I know

This seems like a very specific piece of software so I'm wondering why it has garnered enough votes to make it to the front page - is there something particular about this code base or software program that I should be paying attention to?

It's one of the most popular software packages within the brain MR community. There are many alternatives, but FreeSurfer is one of the first and most robust packages that allows researchers to segment (divide the imaged tissue into classes: white matter, gray matter, cerebral spinal fluid), parcellate (add labels to different brain regions), and generate cortical surface models that can be used to quantify cortical thickness across the human brain.

FreeSurfer is also very influential because it offers a bunch of utility tools for doing analysis/stats on brain images and cortical surfaces, and these tools can be easily combined with other popular neuroimaging software packages.

I’m just here for the phrase “Skullstripping”.

Jokes aside, I think niche software like this is everything HN is about (at least to me). I have no knowledge of MRIs, beyond getting on last year, but seeing this had made me start to research how I would get my brain data back from the NHS to play around with it and see what idiocy I can get up to.

I think, like blender, it overlaps with interests of a lot of people who end up here - an people have done some very cool projects with it.

It's also a good example of something pretty rare: a long lived, decently made and supported project that facilitates a lot of other peoples research.

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